1YI3

Crystal Structure of Pim-1 bound to LY294002


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Pim-1 ligand-bound structures reveal the mechanism of serine/threonine kinase inhibition by LY294002.

Jacobs, M.D.Black, J.Futer, O.Swenson, L.Hare, B.Fleming, M.Saxena, K.

(2005) J.Biol.Chem. 280: 13728-13734

  • DOI: 10.1074/jbc.M413155200
  • Primary Citation of Related Structures:  1YHS, 1YI4

  • PubMed Abstract: 
  • Pim-1 is an oncogene-encoded serine/threonine kinase primarily expressed in hematopoietic and germ cell lines. Pim-1 kinase was originally identified in Maloney murine leukemia virus-induced T-cell lymphomas and is associated with multiple cellular f ...

    Pim-1 is an oncogene-encoded serine/threonine kinase primarily expressed in hematopoietic and germ cell lines. Pim-1 kinase was originally identified in Maloney murine leukemia virus-induced T-cell lymphomas and is associated with multiple cellular functions such as proliferation, survival, differentiation, apoptosis, and tumorigenesis (Wang, Z., Bhattacharya, N., Weaver, M., Petersen, K., Meyer, M., Gapter, L., and Magnuson, N. S. (2001) J. Vet. Sci. 2, 167-179). The crystal structures of Pim-1 complexed with staurosporine and adenosine were determined. Although a typical two-domain serine/threonine protein kinase fold is observed, the inter-domain hinge region is unusual in both sequence and conformation; a two-residue insertion causes the hinge to bulge away from the ATP-binding pocket, and a proline residue in the hinge removes a conserved main chain hydrogen bond donor. Without this hydrogen bond, van der Waals interactions with the hinge serve to position the ligand. The hinge region of Pim-1 resembles that of phosphatidylinositol 3-kinase more closely than it does other protein kinases. Although the phosphatidylinositol 3-kinase inhibitor LY294002 also inhibits Pim-1, the structure of the LY294002.Pim-1 complex reveals a new binding mode that may be general for Ser/Thr kinases.


    Organizational Affiliation

    Vertex Pharmaceuticals Incorporated, Cambridge, Massachusetts 02139, USA. marc_jacobs@vrtx.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proto-oncogene serine/threonine-protein kinase Pim-1
A
273Homo sapiensGene Names: PIM1
EC: 2.7.11.1
Find proteins for P11309 (Homo sapiens)
Go to Gene View: PIM1
Go to UniProtKB:  P11309
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LY2
Query on LY2

Download SDF File 
Download CCD File 
A
2-MORPHOLIN-4-YL-7-PHENYL-4H-CHROMEN-4-ONE
2-(4-MORPHOLINYL)-8-PHENYL-4H-1-BENZOPYRAN-4-ONE
C19 H17 N O3
CZQHHVNHHHRRDU-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
CME
Query on CME
A
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LY2IC50: 820 - 4000 nM (100) BINDINGDB
LY2IC50: 4000 nM BINDINGMOAD
LY2IC50: 4000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.208 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 97.647α = 90.00
b = 97.647β = 90.00
c = 80.725γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
AMoREphasing
d*TREKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-01-25
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description